The 25-year-old Babar clocked 2:50:31 to set the new course record among the Indian women athletes, bettering her own feat of 2:53:35 set in the 2012 edition of the race.
The top Indian male and female finishers in the full marathon (42.19km) received a prize money of Rs 5 lakh each.
Babar, employed with Central Railway, bagged a bonus of Rs 1 lakh for breaking the course record.
In the men's field, it was a close contest with Karan clocking 2:24:08, followed by Rashpal Singh 2:24:38 and Binning Lyngkhoi 2:24:40.
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"More than winning, I wanted to qualify for the Commonwealth Games and Asian Games (both to be held in 2014). I couldn't achieve the qualification time but I am happy that I could achieve the target of 2 hours 50 minutes that I had set for my self," Babar said.
Babar said she participated in the Marathon to have a work out and improve her endurance level for steeplechase.
The Central Railways ticket-checker said she will train harder and perform better at the track and field events to qualify for the two quadrennial extravaganzas.
Karan (24) said his aim was to finish in the third place after securing the fourth spot in the previous edition.
Ram Singh Yadav, who set the host nation-specific course mark (2:16.59) in 2012 to qualify for the London Olympics, dropped out of the race due to knee pain. He hurt his knee in run-up to the event but had recovered nearly a week ago.